This example uses VMD to set up a classical forcefield simulation in CP2K. You can download VMD from here, but it may well already be installed on a machine you can access.

When VMD is running you can download a protein structure using the “extensions → data → PDB database query” dropdown menus of the main VMD window. This allows a PDB structure file to be downloaded (assumes that you have an internet connection on the machine running VMD). You should get a window like

Enter the 4 character accession code of a protein, here I've put in ubiquitin - 1ubq - and select load into a new molecule. You should now see a line representation of the protein in the vmd window. The important step is now to generate a topology for this molecule that defines how it is connected and will define how interactions from the main forcefield we will use will be mapped to the atoms in the molecule we have just downloaded. To do this we can use the autopsf plugin. We select this from the “extensions → modelling → automatic PSF generator” dropdowns of the VMD main window.

Hit I'm feeling lucky. You should now have three new files in the directory where you started VMD (or maybe where it is installed in windows if you haven't changed directory…) 1ubq_autopsf.psf, 1ubq_autopsf.pdb, 1ubq_autopsf.log.

We can easily solvate this in VMD using the “extensions → modelling → Add Solvation Box” dropdowns. Maybe it is a good idea to specify the box size you want, or as I've down a bit of padding to stop the periodic images of the protein getting too close, then hit solvate.

Now you should have solvate.psf and solvate.pdb in your directory, which contain the coordinates and connectivity information of the solvated protein. Open the .psf file edit the first line to simple read PSF. For some proteins you might now need to add ions into the solvent to neutralize the system, but we're OK with ubiquitin.

At this point we're nearly ready to run CP2K. First we need to get hold of the forcefield files. The CHARMM forcefields are distributed from the MacKrell group website charmm_ff.shtml. Download toppar_c31b1.tar.gz, extract it with something like tar -zxvf toppar_c31b1.tar.gz.

OK, finally ready to go. The first thing to do is to carry out a rough minimization to remove any close contacts between the protein and the waters that we added in VMD. These clashes would probably make molecular dynamics unstable if we just started running.

We take the coordinates from previous minimization run using the external restart option in CP2K. Hopefully this works for you and you can explore the MD facilities in the code. You'd need to equilibriate for quite some ns before starting production, maybe including some NPT to make sure the box size is correct.

(This exercise is heavily based on material I-Feng William Kuo (Lawrence Livermore National Laboratory) presented at previous CP2K workshops)